From the initial examination of Tuvix (in the episode of the same name), we learn that flowers had been fused into the new being at the genetic level:

EMH: I'm also picking up traces of a third genetic pattern. It appears to be plant-based.

TUVIX: The orchids. We had collected several dozen samples of orchids. They were in our sample containers when we beamed up.

EMH: Well, they're part of your genetic structure now. But they don't appear to be affecting your biochemistry.

When Tuvix is disintegrated at the end of the episode, we see Neelix and Tuvok reemerge on the bio-bed but not the orchids:

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What happened to the plant DNA?

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    A better question is, what the hell happened to the sample containers the orchids were in when they beamed up the first time? – Valorum Jan 30 '16 at 22:34
  • @Richard : I assume the sample containers are durable plastics made from organic hydrocarbon molecules that were simply absorbed into Tuvix's body and wouldn't have appeared abnormal to the Doctor's scan. – Praxis Jan 30 '16 at 22:53
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    That would explain why a handle came out when he went to the loo. – Valorum Jan 30 '16 at 22:59

The combination of the two DNA strands (Tuvok and Neelix) was not a result of the plant's DNA, but rather the enzymes that were present within the plant material. The DNA from the plant merely seems to have come along for the ride when their DNA (and other biological materials) got jumbled up.

KIM: And if the enzymes that cause symbiogenesis interacted with their DNA while they were in the matter stream, it might have caused their patterns to merge.

As such, the foreign plant DNA was most likely destroyed by the host's immune response, in much the same way that any other foreign DNA would be.

It's fairly telling that when the Doctor is talking about separating them, he's only referring to two DNA strands

KIM: Instead of barium, we've come up with a radioisotope that attaches itself to the DNA of one of the merged species, but not the other.

EMH: Then we simply beam out the selected DNA and segregate the two merged species.

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    This seems to ignore the Doctor's statement, "Well, they're part of your genetic structure now." – Praxis Jan 30 '16 at 23:07
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    @Praxis - I didn't write the thing. Heck, sometimes I like to pretend this one never even happened. – Valorum Jan 30 '16 at 23:08
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    It looks like they forgot about the triple genetic structure about halfway through the episode. Agreed: the episode is near the bottom of the barrel. – Praxis Jan 30 '16 at 23:09

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